To your last point "xinteract produced this error", xinteract just spins up other programs in turn, The crash you are seeing is indeed in "/mnt/sanfs/APCF-PROD/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi", which xinteract caused to be run in order to index the pepXML file that came out of peptideProphet. When that crashed, xinteract exited - but xinteract didn't crash, Perhaps a minor distinction, but as you called it out it's probably worth clearing up.
Brian On Wed, Jun 9, 2010 at 11:25 PM, Simon Michnowicz <[email protected]> wrote: > David, > I am not using the Petunia interface, but command-line commands,and > have just used a different naming convention. This has not been an > issue with other files we have run in the past. > > The process is this: > (1)A 4GByte Agilent Data Directory (.d) was converted to a mzXML file > via msconvert. > (2)This mzXML file was converted to mgf using mzXML2Search. > (3)The mgf file was submitted to Mascot for searching. > (4) The resulting .dat file was submitted to Mascot2XML to create a > peptideXML file (this process uses the mzXML file) > (5)This peptideXML file was submitted to peptide Prophet using the > xinteract command. > > There were several cascading issues in this process. > -mzXML2Search produced a very small file compared with the what might > be produced if msconvert --mgf option was used. I am still > investigating why this is happening. > -The Mascot result file yielded very few proteins (~20) with very low > scores > -The pepXML file has only a small number of entries (~10) > -xinteract produced this error. > > Thanks for any suggestions you might have > > regards > Simon > > > > > On Jun 10, 1:46 am, David Shteynberg <[email protected]> > wrote: >> Hi Simon, >> >> This error indicates that the PepXMLViewer failed when it tried to >> index your pepxml file. .pepprophet.xml is not a normal extension >> produced by the TPP for a pepXML file. Can you describe exactly how >> you arrived at this pepXML file? >> >> Thanks, >> -David >> >> On Wed, Jun 9, 2010 at 1:46 AM, Simon Michnowicz >> >> >> >> <[email protected]> wrote: >> > Dear Group, >> > I ran xinteract on a pepXML file that was generated from a Mascot >> > search, and it exited with an error message. >> >> > command "/mnt/sanfs/APCF-PROD/APCF_WEB/tpp/cgi-bin/PepXMLViewer.cgi - >> > I /mnt/sanfs/APCF-PROD/results/tpp/2010-06-08/simon- >> > J2468.pepprophet.xml" exited with non-zero exit code: 11 >> >> > I am afraid I do not know what this error means. I found the input >> > pepXML only had a few number of entries, so am I right to think that >> > this is cause of the error?(The Mascot search was done using >> > incorrect parameters, resulting in a poor output) >> > I have two questions: >> > (1) How much data do you need to provide a satisfactory run for >> > peptideProphet? Is it possible to check this before calling xinteract? >> > (2) I looked at the .dat=>pepXML conversion via Mascot2XML. I expected >> > a 1:1 mapping for proteins, however I found only a subset of proteins >> > being placed in the file. Is there some internal filtering that occurs >> > here? The scores were all low, which might have taxed any algorithm to >> > do this. >> >> > Much thanks for any assistance. >> > Simon Michnowicz >> >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "spctools-discuss" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]. >> > For more options, visit this group >> > athttp://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
